A project template for computational biology, especially bioinformatics
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README.md


title: "Computation Biology Project Template" author: "Byron J. Smith" ...

Introduction

In order to make projects more rational, here is a standard project structure which is intended to be a superset of most computational biology projects.

A git repository which implements this template is available on Github.

License

This work is licensed under the terms of the MIT license:

Copyright (c) 2014-2015 Byron J. Smith

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Quick Start

# Clone a project or project template
git clone http://github.com/bsmith89/compbio-template new-project
# ---OR---
git clone http://github.com/USERNAME/extant-project new-project

cd new-project

# Initialize the project
make init
# You'll be asked if you want to mangle the git repository, removing the
# remote and sqaushing all of the template's history into one commit.

Example Workflow

# Name the project; write a description;
# create a preliminary list of objectives.
vim doc/NOTE.md

# Download raw data from an online repository
cd raw/
curl -O http://mydata.com/raw/seq.tgz
tar -xzvf seq.tgz
cd ..

# Write a thorough description of the raw data
vim doc/NOTE.md

# Write a recipe (or two) to recreate the download protocol
vim Makefile

# Move and standardize naming of data files.
cp raw/seq/sample1.fn seq/sample001.fn

# Move and reformat the metadata.
cat raw/seq/metadata.tsv | sed '1,1d' > meta/samples.tsv

# Write makefile recipes for these operations.
vim Makefile

# Describe and commit progress
vim doc/NOTE.md
git add Makefile doc/NOTE.md
git commit -m "Downloaded and described data."

# Run data through an analysis pipeline (e.g. an all-by-all BLASTx)
makeblastdb -in seq/sample001.fn -input_type fasta
blastx -db seq/sample001 -query seq/sample001.fn \
       -outfmt '6 qseqid sseqid evalue'
       -out res/sample001.all_way.blastx_out
vim Makefile  # Write makefile recipes for the above.

# Prototype an analysis on this data.
ipython3 notebook

# Describe what was done, including an output figure.
vim doc/NOTE.md
mv fig/histogram.png doc/static/2014-11-17_fig1.png

# Commit this progress
git add doc/static/2014-11-17_fig1.png doc/NOTE.md
git commit -m "Updated notes with a prototyped analysis."

# Write a script to do this analysis reproducibly
vim bin/analysis.py
chmod +x bin/analysis.py
cat res/sample001.all_way.blastx_out \
    | bin/analysis.py
    > res/sample001.all_way.blastx_out.analysis.tsv

# Add a recipe to run the analysis
vim Makefile
git add bin/analysis.py Makefile
git commit -m "Script to carry out analysis."

# Additional analysis
# ...
# ...

# Publish the project to github
git remote add origin git@github.com:USERNAME/new-project.git
git push -u origin

User Guide and Project Structure#

Requirements

Optional: dependency diagram

  • Graphviz

Optional: tags

Notes Files

All files which describe the project are version controlled.

Notes files are written in (and make copious use of) Pandoc Markdown, a superset of strict Markdown, and may be compiled for reading. (A recipe to compile markdown files into HTML is defined in the Makefile.)

This default recipe includes a script for rendering LaTeX math in attractive typeset. This should work—as long as there's an internet connection—for either inline math ($\chi^2$, for instance) or blocks of math:

$$ \chi^2 $$

doc/NOTE.md

: This is the core notebook for the project. All experiments and conclusions should be clearly described in the "Notebook" section. Along with the project's Makefile, this notebook should allow a 3rd party to run and understand the entire analysis which was carried out.

doc/TEMPLATE.md

: This file, describing how to use the template and the project's directory structure.

doc/static/

: Files (usually images) which are included in notebooks. These files are version controlled, so that a remote repository (e.g. github) can compile the notebook with the images. Despite being version controlled, they should never change: no diffing binary data! Future analysis may completely remove the workflow which produced these files, but, in order to record the research process, the results are maintained in this folder. Static file names should be prefixed with the date in YYYY-MM-DD format.

doc/static/main.css

: Used in the compilation of HTML versions of notes written in markdown.

Code

All project code is version controlled.

Makefile

: Ideally, the entire analysis. Reproduce the full analysis with a single command:

```bash
$ make all

```

Any data processing which is computationally intensive should save
intermediate files in order to utilize `make`'s piece-wise build.

Sensitive data should not be included in `Makefile`, since that
file is frequently version controlled.  Instead `local.mk` is `included` so
that sensitive values can be included and then referenced as variables.

Also, auto-dependency generation is a very neat feature.
See [here](http://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#include).
With this feature of GNU Make, more complex dependency structures,
(like all-by-all comparisons) can be generated.

etc/

: While not strictly code, the etc/ directory is a place to store version controlled data which cannot be regenerated automatically, but which is needed for the workflow regardless of the data in raw/.

The best example of something that should go in this directory are
primer sequences.  Contents of `etc/` are version controlled, unlike
raw data.

bin/

: Executable files which carry out any parts of the pipeline requiring more than a Makefile recipe. These scripts (and source code to be compiled) are version controlled, unlike data files. Scripts should be well documented.

 -  Required: Each script has a docstring (comment at the top after the
    shebang) which describes the use of the script from the command line.
 -  Good: Scripts are well commented, explaining the logic of any difficult
    to understand code.
 -  Great: Scripts are designed with full help text, conforming to POSIX
    standards.

Scripts should take any data which only needs to be used once from STDIN.
If this can be accomplished in multiple ways, one rule of thumb is for
scripts to take the largest files (usually a sequence file) from STDIN and
smaller metadata files as positional arguments.
This is designed to make streaming pipelines an easy transition.

Scripts should be designed for portability.

 -  Good: Scripts accept all input data externally.
    Data files are _not_ hard coded into the script.
 -  Great: Variable parameters of the analysis are accepted as positional
    arguments, and options.
    Logical defaults are acceptable.
    Parameters are _not_ hard-coded into the scripts.
 -  Greatest: Scripts are constructed in a modular design.
    e.g. Python scripts divide logical chunks into "public" functions so
    that those parts can be imported by other scripts.

Scripts for which all of these recommendations are met,
and where the routine may be useful in other projects,
are great candidates for inclusion in the `bin/utils/` ~~submodule~~.

PBS submission scripts should be stored in `bin/pbs`, and those
which produce figures, `bin/fig`.

Any analysis scripts that can be used by other projects should ultimately
end up in the sequtils
[python package](https://github.com/bsmith89/compbio-scripts).
One way to develop this package in parallel with the template or a project
is to clone <https://github.com/bsmith89/compbio-scripts> and replace your
installation of sequtils with a development install.

```
source .venv/bin/activate
pip install -e path/to/clone
```

bin/fig/

: Executable scripts which normally:

 -  Produce figures in PDF format, saving them to `fig/`;
 -  Require intermediate results in a tabular format, saved in `res/`;
 -  Usually have a name which is identical to or a substring of the figure
    produced.

bin/pbs/

: Scripts to be submitted to the PBS batch computing system (qsub). These are used to carry out computationally intensive steps in the analysis pipeline. They do not replace, however, Makefile as a complete description of the pipeline. Perhaps best practice would be to just set up the environment and then run make directly...?

e.g. `example.pbs`:

```bash
#!/usr/bin/env sh
#PBS -V
#PBS -m a
#PBS -l nodes=4:ppn=4,walltime=10:00:00,pmem=500mb

# Change to the directory from which the job was submitted.
cd ${PBS_O_WORKDIR}

# Run make to produce a particular output.
make tre/computationally_difficult.nwk
# Consider using make's '-o' flag to prevent regenerating requirement
# files.

```

ipynb/

: IPython notebooks, useful for fast prototyping and exploratory analysis. In there raw form, they are not good for version control, since they include a bunch of the output data in the same file. They are also not conducive to reproducing a result after external files and directories have been changed. This is largely because they have file paths hard-coded in. IPYNBs should be used kinda like the doc/NOTE.md; They are a record of a thought-process/workflow, but are not guarenteed to execute the same way after subsequent commits. Instead, important analyses should be ported over to version controlled scripts, and ideally included as recipes in Makefile.

Before being committed to git, IPYNBs should have their output and line
numbers wiped, so as to avoid committing binary data, or arbitrary changes;
re-running a notebook shouldn't change it in the eyes of git.
To do this in an automated fashion, a clean/smudge filter has been included
in `bin/utils`, and the initalization recipes in Makefile configure git to
run the filter when staging files to be commited.
While this won't erase the output from the local copy of the notebook,
forks of the project will get an 'un-run' version.
Notebook which do not fit the glob pattern `ipynb/*.ipynb` will not be
filtered, so static versions of notebooks with output included can be
moved to `doc/static/` and version controlled.

IPython has been configured (see `ipynb/profile_default/` below)
so that starting a notebook server from the
command line will look for `*.ipynb` files in `ipynb/`,
but the working directory will be set back to the root directory when a
notebook is loaded.
Just calling `ipython3 notebook` from the root directory is best.

Configuration and Environment

All configuration files are version controlled.

Distributing configuration files with the template, and version-controlling them in projects allows customization of components in just one place. Anyone who forks the template or any project based on it will then have the same configuration.

.initialized

: Empty file used to signal whether or not the project has been initialized. The file is created on running make init, which adds the IPython notebook filter to the project's git configuration, makes a new Python virtual environment (.venv/), and installs everything in requirements.pip to .venv.

Unlike the other configuration files in this template,
`.initialized` is ignored by git.

ipynb/profile_default/

: A custom IPython profile which changes a few things from the built-in default:

 -  IPython notebooks display figures inline by default;
 -  The default editor is full `vim`;
 -  Tab completion is more like `bash`;
 -  Running `ipython3 notebook` from the command line is convenient:
     -  The server look for notebook files in the `ipynb/` subdirectory;
     -  When loaded, the working directory for the notebook is automatically
        changed to the root of the project (i.e. `cd ..`).

See
[IPython's documentation][ipy-config].

[ipy-config]: <http://ipython.org/ipython-doc/dev/config/intro.html>

.gitattributes / .gitignore / .gitmodules

: Configuration files for git.

requirements.pip

: Packages installed to the python virtualenv on make python-reqs. To make it easier for others to re-run your scripts, rather than using pip install [package] or similar, instead add the package to this file. Then make python-reqs.

Data

Data is not version controlled.

raw/

: All of the raw data and metadata needed to recreate the entire analysis. This should be kept in the exact same format as it is available publicly; if you're going to rename files, remove header lines, or reformat, these processed versions of the data should be stored in directories other than raw/. While raw data files are not version controlled, they should all be available in an online repository. The raw data appendix, in doc/NOTE.md, describes everything a third party (or the author a month later) needs to know about the raw data.

 -  Required: Describes (in detail) where all of the data came from.
 -  Good: Instructions for retrieving all of the data from an online
    repository.
 -  Great: Recipe for data retrieval included in `Makefile`.

It is also advisable to save data in directories named by the date it was
collected, or the date of the experiment
so growth curves started on October 20th, 2014, would be stored in
`raw/2014-10-20/growth-curve.csv`, and
`doc/NOTE.md` would describe the experiment and this file in detail.

Intermediate data files are separated into directories based on their content. The extension portion of these file names should indicate the format of the data, while the '.' separated words which make up the file name loosely describe the workflow used to produce the file. For example:

  • seq/16S.align.ungap.afn would be multiple sequence alignment (.align.) in nuceotide FASTA format (.afn) which has had all gap positions removed (.ungap.).
  • tre/16S.align.ungap.nwk is a Newick formatted phylogenetic tree generated from seq/16S.align.ungap.afn.

meta/

: All of the experiment metadata, formatted conveniently for downstream analysis. Tab separated values (.tsv) with headers is the preferred format. The files in this directory are usually minimally processed versions of the original metadata files stored in raw/. Column titles should be explained in the metadata appendix in doc/NOTE.md.

seq/

: Intermediate analysis files which contain sequence.

tre/

: Intermediate analysis files which contain phylogenetic or taxonomic trees.

res/

: Any intermediate results which cannot be easily placed in another directory. For instance, a TSV of pairwise sequence distances.

Final Results

Final results are not version controlled.

fig/

: All 'final' output from an analysis, usually figures or tables. Figures don't have to be good enough for a publication, they just have to represent the culmination of an analysis.

Filename Conventions

These conventions may vary from project to project. The naming scheme is not a replacement for both liberal note-taking and a programmatic description of the pipeline in the Makefile.

File Formats

suffix meaning comments
list list of values one item per line
tsv tab separated values see pandas
csv[^csv-tsv] comma separated values see pandas
fn unaligned nucleotide sequence see Wikipedia
fa unaligned amino acid sequence
afn aligned nucleotide sequence indels as '-' [^align-fmt]
afa aligned amino acid sequence
nwk Newick formatted binary tree see Wikipedia

[^csv-tsv]: TSVs with column titles are preferred (because they're easier to inspect manually), but CSVs are acceptable. [^align-fmt]: Alignment software has several standards for indicating indels. Here, somewhat arbitrarily, '-' is the preferred symbol.

Processing Flags

infix meaning comments
head/tail top and bottom entries part of dataset, meant for testing
align aligned by homology a variety of tools are available
ungap gap only positions removed
codon codons aligned this is usually done via back-align

TODO

  • Testing framework
  • Fill in common file conventions
  • SHA-1 checksum for data files
  • Package scripts in a different repo?
  • template branch?